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Stage 2 Chemistry > Topic 3 - Organic Chemistry > Flashcards

Topic 3 - Organic Chemistry Flashcards

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1
Q

What is organic chemistry?

A

Organic chemistry is the study of carbon (organic) compounds.

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2
Q

What are some key features of carbon that validify its presence in all organic compounds?

A

The ability of carbon to form so many compounds is unique among the elements. Carbon has a covalence shell consisting of four electrons. It may form single, double or triple bonds with other carbon atoms and form straight chains, branched chains or rings.

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3
Q

What are the three different types of structural formulae?

A

Extended structural formula, condensed structural formula, and skeletal structural formula.

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4
Q

What is systematic nomenclature?

A

Systematic nomenclature is the chemical system used to help identify the structure of a compound. The name given through this system provides information about carbon chain length, functional groups, and the positioning of functional groups.

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5
Q

What are the prefixes for carbon chain length?

A

1 - meth
2 - eth
3 - prop
4 - but
5 - pent
6 - hex
7 - hept
8 - oct
9 - non
10 - dec

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6
Q

What is the suffix used for carboxylic acids?

A

-oic acid

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7
Q

What is the suffix used for carboxylate ions?

A

-oate ion

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8
Q

What is the suffix used for esters?

A

-yl -oate

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9
Q

What is the suffix used for amines?

A

-amine

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10
Q

What is the suffix used for amides?

A

-amide

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11
Q

What is the suffix used for alkanes?

A

-e

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12
Q

What is the suffix used for alkenes?

A

-ene

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13
Q

What is the suffix used for alcohols?

A

-ol

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14
Q

What is the suffix used for aldehydes?

A

-al

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15
Q

What is the suffix used for ketones?

A

-one

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16
Q

What is a branching alkyl chain?

A

Anything carbon based that is attached to the longest carbon chain is considered a branching alkyl chain.

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17
Q

What are single carbon bonds called and what wording is used?

A

Alkanes: C-C
-ane-

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18
Q

What are double carbon bonds called and what wording is used?

A

Alkenes: C=C
-ene-

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19
Q

What are triple carbon bonds called and what wording is used?

A

Alkynes: C=-C
-yne-

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20
Q

What identifies an alcohol functional group?

A

-O-H

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21
Q

How do you name a molecule with multiple alcohol functional groups?

A

State the number location of both alcohols (after the overall molecule name) with the relevant prefix (di, tri, etc) and -ol.
EXAMPLE: butane-2,4,-diol

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22
Q

What is an isomer?

A

When molecules have the same molecular formula but with a different structure.

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23
Q

What does the degree of saturation refer to?

A

The number of hydrogens (number of single bonds between carbon atoms).

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24
Q

What does the degree of unsaturation refer to?

A

The number of double or triple bonds between carbon atoms.

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25
Q

What does degree of saturation/unsaturation mean for the melting points of molecules?

A

Molecules that contain only single bonds (saturated) can stack neatly, forming stronger dispersion forces between molecules. Therefore, saturated molecules will have higher melting/boiling points and are more likely to be solids at room temperature.

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26
Q

How are alcohols classified as primary, secondary or tertiary?

A

The primary, secondary or tertiary nature of alcohols refer to the number of carbon atoms which the carbon atom attached to the hydroxyl group is bonded to.
One = Primary
Two = Secondary
Three = Tertiary

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27
Q

How is the oxidation of alcohols used to distinguish between primary, secondary and tertiary alcohols?

A

In organic chemistry, oxidation refers to the addition of or increase in the number of oxygens. Acidified dichromate is an oxidant which allows primary and secondary alcohols to be distinguished from tertiary alcohols, by changing colours. Primary and secondary alcohols can undergo oxidation, causing the acidified dichromate (orange) to be reduced to chromium ions (green). Tertiary alcohols cannot be oxidised using acidified dichromate, meaning there is no colour change and the solution remains orange.

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28
Q

What happens when acidified dichromate is combined with a primary alcohol?

A

Colour change from orange to green.

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29
Q

What happens when acidified dichromate is combined with a secondary alcohol?

A

Colour change from orange to green.

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30
Q

What happens when acidified dichromate is combined with a tertiary alcohol?

A

No colour change from orange to orange.

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31
Q

Write an equation to show the reduction of acidified dichromate when combined with a primary or secondary alcohol, to produce the colour change from orange to green.

A

Cr2O7-2 + 14H+ + 6e- —> 2Cr+3 + 7H2O

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32
Q

What does the oxidation of a primary alcohol result in?

A

Primary Alcohol —> Aldehyde —> Carboxylic Acid

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33
Q

What does the oxidation of a secondary alcohol result in?

A

Secondary Alcohol —> Ketone

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34
Q

When does the oxidation of alcohols stop?

A

The oxidation of alcohol stops at the point where there are no more hydrogens to be liberated that provide oxidation (attach an oxygen).

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35
Q

What is a carbonyl group?

A

A carbonyl group is a double bond between a carbon atom and an oxygen atom (C=O).

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36
Q

What do aldehydes and ketones have in common?

A

Both contain a carbonyl group (C=O).

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37
Q

What functional group is present on an aldehyde?

A

A double bonded oxygen that is in the terminal position (at the end of the molecule).

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38
Q

What functional group is present on a ketone?

A

A double bonded oxygen that is present in the middle of the molecule.

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39
Q

How are aldehydes and ketones formed?

A

Aldehydes are formed from the oxidation of primary alcohols. Ketones are formed from the oxidation of secondary alcohols.

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40
Q

What happens during the oxidation of an aldehyde under acidic versus basic conditions?

A

The oxidation of an aldehyde under acidic conditions forms a carboxylic acid. Whereas, the oxidation of an aldehyde under alkaline (basic) conditions forms a the carboxylate ion (deprotonated carboxylic acid/salt of a carboxylic acid).

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41
Q

What are the experiments used to oxidise aldehydes in acidic versus basic conditions?

A

Acidified dichromate can oxidise aldehydes into carboxylic acids under acidic conditions. Tollen’s reagent can oxidise aldehydes into carboxylate ions under basic conditions.

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42
Q

How do you differentiate between aldehydes and ketones?

A

Structurally, aldehydes contain their double bonded oxygen (C=O) in the terminal position whereas ketones contain it within the chain. Tollen’s reagent with an aldehyde forms silver deposition, whereas ketones will not form silver.

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43
Q

What are carbohydrates?

A

Carbohydrates are naturally occurring sugars and their polymers.

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44
Q

What is the general formula used for all carbohydrates?

A

CxH2yOy

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45
Q

What is a simple sugar unit composed of?

A

A simple sugar unit contains either a ketone or aldehyde functional group, as well as multiple hydroxyl groups.
Refer to as polyhydroxyaldehydes or polyhydroxyketones.

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46
Q

What is glucose classified as and why?

A

Glucose is a polyhydroxyaldehyde because it contains an aldehyde within its structure and follows the general carbohydrate formula.

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47
Q

What is fructose classified as and why?

A

Fructose is a polyhydroxyketone because it contains a ketone within its structure and follows the general carbohydrate formula.

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48
Q

What can carbohydrates become due to their functional groups?

A

Due to the functional groups within carbohydrates, they pose the ability to polymerise (form polymers).

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49
Q

What are monosaccharides?

A

Single unit carbohydrates.

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50
Q

What are disaccharides?

A

Two carbohydrates conjoined.

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51
Q

What are polysaccharides?

A

Polymers of repeating carbohydrate units.

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52
Q

How do you identify repeating carbohydrate units?

A

The oxygen that is single bonded to two carbons, separating two carbohydrates, can be used to distinguish the repeating unit for saccharides.

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53
Q

What are the two forms that saccharides can exist in?

A

Cyclic (ring) or linear (chain) form.

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54
Q

For monosaccharides, how does cyclic form influence its reaction abilities.

A

In cyclic form, the molecule does not have the aldehyde or ketone. This means it will not react with Tollen’s reagent.

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55
Q

Why are monosaccharides solid at room temperature?

A

Monosaccharides are solid at room temperature due to the large amounts of hydrogen bonding between hydroxyl groups. This means a substantial amount of energy would be required to disrupt these bonds, such as heat, justifying its structure of solid at room temperature.

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56
Q

How are disaccharides formed?

A

A condensation reaction (producing water) between two cyclic monosaccharides, which removes a hydroxyl group from one and a hydrogen atom from the other to allow them to be joined by bonding through an oxygen atom.

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57
Q

How are disaccharides broken down?

A

A hydrolysis reaction (consuming water) of a disaccharide to split it into two monosaccharides. Water is combined and joins a hydroxyl group to one and adds a hydrogen to the oxygen on the other, to form a hydroxyl group.

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58
Q

How are polysaccharides formed?

A

Polysaccharides are formed by condensation reactions of many monosaccharides catalysed enzymatically.

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59
Q

How are polysaccharides broken down?

A

Polysaccharides can be broken down into mono, di and trisaccharides by hydrolysis with water and an enzyme.

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60
Q

How is the repeating unit of a polysaccharide identified?

A

The repeating unit of a polysaccharide can be identified the same way as the repeating monomer of a polymer:
- It has to be “copied and pasted” immediately down the chain
- The repeating unit (monomer) is shown using brackets
- The structural formula of the monomer can be drawn from the repeating unit by identifying the two bonds that are hydrolysed

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61
Q

What is the general equation for the hydrolysis of a polysaccharide?

A

(CxH2yOy)n + nH2O —> nCxH(2y+2n)O(y+n)

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62
Q

Are monosaccharides, disaccharides and polysaccharides soluble in water?

A

Monosaccharides are most soluble in water as their molecular weight is smaller, meaning there are less dispersion forces between the molecules (despite having more functional groups per unit). Disaccharides also tend to be soluble in water, due to weak dispersion forces between molecules. However polysaccharides are not usually soluble in water as the dispersion forces between molecules are significant.

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63
Q

What property of carbon enables its widespread presence in organic compounds?

A

Carbon has a covalence of four meaning it may form single, double or triple bonds with other carbon atoms, as well as form straight straight chains, branched chains or rings.

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64
Q

What are the characteristics of monosaccharides and disaccharides that enable their solubility in water?

A
  • Many polar hydroxyl groups (-OH) that can undergo extensive hydrogen bonding with polar water molecules
  • Small molecule = weaker secondary (dispersion) forces, therefore easily separated in water
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65
Q

What are the characteristics of polysaccharides that enable their insolubility in water?

A
  • Many polar hydroxyl groups (-OH) that can undergo extensive hydrogen bonding with polar water molecules
  • Larger molecules = stronger secondary (dispersion) forces, therefore, harder to separate polysaccharide molecules in water
66
Q

What are carboxylic acids?

A

Carboxylic acids contain a carboxyl functional group (-COOH) at the end of the carbon chain.

67
Q

What are carboxylic ions?

A

The deprotonated version of the carboxylic acid is a carboxylate ion (-COO-).

68
Q

How are carboxylic acids formed?

A

Carboxylic acids can be produced by the oxidation of primary alcohols or aldehydes using an oxidising agent and heat.

69
Q

Why are carboxylic acids classified as weak acids?

A

Carboxylic acids are weak due to their long carbon chain attached to the COOH functional group. This means they partially ionise (form ions) within water. The process of ionisation is in equilibrium that favours the left direction and, thus, only a small portion of carboxylic acid molecules ionise to form carboxylate ions.

70
Q

What is the equation for the neutralisation of carboxylic acid with hydroxide?

A

RCOOH + OH- ⇌ RCOO- + H2O

71
Q

What is the equation for the neutralisation of carboxylic acid with carbonate ions?

A

RCOOH + CO3 2- ⇌ RCOO- + CO2 + H2O

72
Q

What is the equation for the neutralisation of carboxylic acid with hydrogencarbonate ions?

A

RCOOH + HCO3 - ⇌ RCOO- + CO2 + H2O

73
Q

What does the neutralisation of carboxylic acids produce?

A

These neutralisation reactions occur fast at room temperature and are exothermic.
Carbonate and hydrogencarbonate reactions produce carbon dioxide leading to effervescence (bubbling) occurring.

74
Q

Are carboxylate ions soluble in water? Why or why not?

A

Carboxylate salts are ionic compounds composed of a carboxylate ion and cation. The negatively charged carboxylate ion can undergo ion-dipole interactions with the partial position dipole on polar water molecules.

75
Q

Are carboxylic acids soluble in water? Why or why not?

A

Carboxylic acids can only form hydrogen bonds with adjacent water molecule. Hydrogen bonds are weaker intermolecular interactions than ion-dipole bonds. This is because the charge of an ion is much stronger than the partial charge on a dipole, meaning stronger electrostatic attraction for the ion. Therefore, large organic molecules with carboxylic acid functional groups are likely to be insoluble in water.

76
Q

What is an amine?

A

An amine is any organic compound containing the (-N-) functional group.

77
Q

What is the simplest amine?

A

The simplest amine is ammonia. All other amines are considered as derivatives of ammonia with one or more hydrogens replaced by an alkyl group/hydrocarbon chain.

78
Q

How do you classify amines as primary, secondary or tertiary?

A

This classification refers to the number of carbon chains that the nitrogen atom is bonded to. Primary amines have the nitrogen atom bonded to one R group, whereas secondary are bonded to two and tertiary are bonded to three.

79
Q

Do amines act as acids or bases? Why?

A

Nitrogen atoms in an amine contains a non-bonded electron pair which can accept a hydrogen ion acting as a base. The resulting protonated form of the amine is called an ammonium ion. It has a positive charge and can dissolve in water.

80
Q

Are amine salts soluble in water? Why or why not?

A

Amine salts are ionic compounds composed of an ammonium ion (protonated amine/additional hydrogen) and some anion. Due to the positively charged ammonium ion, they can undergo ion-dipole interactions with polar water molecules as the positively charged ammonium ion attracts the negative dipole of water molecules.

81
Q

Are amines soluble in water? Why or why not?

A

Amines (not protonated) can only form hydrogen bonds with adjacent water molecules which are weaker than ion-dipole bonds. Therefore, small amines may be soluble in water but larger molecules will not.

82
Q

How do you convert an amine into an amine salt to make it soluble in water?

A

Amines are converted into amine salts by protonating them (adding a hydrogen atom) and some anion.

83
Q

What are esters?

A

An ester is organic molecule containing the ester (-COO-) functional group.

84
Q

How are esters formed?

A

Esters are formed from reactions between alcohols and carboxylic acids (esterification or condensation). The carbon chains on either side of the ester group are from the carboxylic acid and alcohol. The R group attached to the carboxyl (-C=O) end come from the carboxylic acid. The other R group, attached to the –C-O- end, comes from the alcohol.

85
Q

How are esters named?

A

Esters are named using the alcohol prefix followed by the carboxylic acid prefix:
1. Alcohol prefix forms the first part of the name with the “-yl” suffix, for example, methanol changes to methyl.
2. The carboxylic acid suffix changes from –oic to –olate, for example, ethanoic acid changes to ethanoate.

86
Q

What are the conditions required for the formation of esters?

A

Organic reactions are typically slow at room temp and require heating for long periods. Heating reaction increases the reaction rates to achieve a satisfactory yield. The reactants and products are volatile (have low boiling points) due to their inability to form hydrogen bonds independently, and will vaporize with heating causing them to be lost from the reaction vessel.

87
Q

What is reflux and how is it used for ester production?

A

The reactants and products of ester production are volatile (have low boiling points) and will vaporize with heating causing them to be lost from the reaction vessel. Reflux apparatus is used to overcome this. It allows reactants to be heated over a long period of time without minimal loss due to evaporation of reactants/products. Vapors from the pear-shaped flask rise into the condenser which cools them back to a liquid and return it to the reaction mixture. In esterification reactions, trace amounts of concentrated acid are also used as a catalyst.

88
Q

What is the reverse process of condensation?

A

Ester hydrolysis is the reverse process of condensation reactions. An ester can be hydrolysed (combined with water) to produce a carboxylic acid and alcohol. The products of ester hydrolysis are different depending on whether the reaction takes place in acidic or basic conditions.

89
Q

What does ester hydrolysis under acidic conditions?

A

The products ester hydrolysis in acidic conditions are a carboxylic acid and alcohol.

90
Q

What does ester hydrolysis under basic conditions?

A

The products of ester hydrolysis in basic conditions are a carboxylate ion and alcohol.

91
Q

What are amides and why are they important?

A

Amides are organic molecules with the amide (-CONH-) functional group. They are important in nature as they form the links between amino acids in proteins.

92
Q

How are amides formed?

A

A condensation reaction (water is produced) between a carboxylic acid and an amine leads to the formation of an amide. Water is formed from the –OH group of the acid and a hydrogen atom from the amine.

93
Q

What are the products of amide hydrolysis in acidic conditions?

A

The products of amide hydrolysis in acidic conditions are a carboxylic acid and a protonated amine.

94
Q

Are amide groups basic? Why or why not?

A

Amide groups are not basic because the lone pair on nitrogen is locked by the hydrogen.

95
Q

What are the products of amide hydrolysis in basic conditions?

A

The products of amide hydrolysis in basic conditions are a carboxylate ion and an amine.

96
Q

What are triglycerides?

A

Triglycerides are fats and oils derived from plants and animals. They are trieseters (molecules containing three ester functional groups) formed from the reaction of propane-1,2,3-triol (glycerol) and three long, straight chain carboxylic acid (called “fatty acids”).

97
Q

What is transesterification?

A

Transesterification is the simultaneous cleaving and forming of ester bonds.

98
Q

Are triglycerides soluble in water? Why or why not?

A

Due to the large lengths of carbon chains on the fatty acids, triglycerides are insoluble in water and soluble in non-polar/organic solvents (dispersion forces are much stronger). The ester groups they contain are not particularly polar as they can only form dipole-dipole forces.

99
Q

What are dispersion forces?

A

Dispersion forces are momentarily induced dipole forces due to electrons.

100
Q

What are the characteristics of saturated fatty acids?

A
  • Contain only single bonds, therefore have straight carbon chains
  • Pack together closely, increasing dispersion forces
  • Higher melting points and therefore solids at room temp
101
Q

What are the characteristics of unsaturated fatty acids?

A
  • Contain at least one double or triple bonds and have kinks in the carbon chain
  • Pack together less closely, decreasing dispersion forces
  • Lower melting points and therefore liquids at room temp
102
Q

How can the presence of alkenes be identified?

A

Alkene functionality allow unsaturated triglycerides to undergo reactions with group seven elements (chlorine, iodine, bromine, or hydrogen). When the brown bromine solution is added to a solution of unsaturated molecule, a loss of colour is observed. If there is no change of colour is observed than the molecule is already saturated.

103
Q

How can the degree of unsaturation be measured?

A

The degree of unsaturation of a triglyceride can be measured by determining the mass of bromine that reacts with a triglyceride. Another way to determine the degree of unsaturation of a triglyceride is to measure the iodine number. A higher mass of iodine (I2) that reacts with 100g of a triglyceride means a higher degree of unsaturation.

104
Q

What is hydrogenation?

A

Hydrogenation is a process used to convert liquids and oils into solid fats by reducing the degree of unsaturation. This is the process used to turn oil to margarine. Decreasing the number of double bonds, increases the dispersion forces (less kinks in the chain). The process of hydrogenation is simply an alkene addition reaction with hydrogen being added to the alkene, breaking the alkene and inserting hydrogen.

105
Q

What are the conditions of hydrogenation?

A

Hydrogenation is an addition reaction in which hydrogen gas is added across a carbon-carbon double bond. This process is really slow at room temperature. Thus, it is carried out at high temperatures, high pressures, and in the presence of a Nickel based catalyst.

106
Q

What are the products of hydrogenation?

A

The final product may still have some degree of unsaturation but will be a solid at room temp. Reducing kinks in chain increases dispersion forces consequently decreasing melting point and boiling points.

107
Q

What does the hydrolysis of triglycerides produce in acidic conditions?

A

The products are glycerol (propane-1,2,3-triol) and three carboxylic acids.

108
Q

What does the hydrolysis of triglycerides produce in basic conditions?

A

The products are glycerol (propane-1,2,3-triol) and three carboxylate ions.

109
Q

What are the conditions of natural hydrolysis of triglycerides versus the laboratory conditions?

A

The hydrolysis of triglyceride is carried within humans utilising the enzyme Triacylglycerol lipase. Whereas, in the laboratory, high temperatures and either concentrated acidic or basic solutions are required to perform a hydrolysis reaction.

110
Q

Where might micelles be formed?

A

After the hydrolysis of triglycerides under basic conditions, as carboxylate ions are produced.

111
Q

How does the structure of carboxylate ions allow them to form micelles?

A

The carbon chain tail of the carboxylate ions is non-polar (neutral) and hydrophobic. The head of the carboxylate ion is anionic (negatively charged) and hydrophilic.

112
Q

How are micelles formed generally?

A

The long non-polar hydrocarbon chain of carboxylic ions is hydrophobic, and the anionic head is hydrophilic. When agitated within water, the tails point inwards due to their hydrophobic nature, whilst the head position themselves outwards because they want to form ion-dipole interactions with the aqueous solution. Thus, the carboxylate ions arrange themselves to form micelles containing a non-polar core and a polar surface.

113
Q

Is glucose an aldehyde or ketone?

A

Aldehyde.

114
Q

Is fructose an aldehyde or ketone?

A

Ketone.

115
Q

How are micelles formed in relation to soap and grease?

A

Soap is a common surfactant used to form micelles around oil particles. The hydrophobic tails penetrate oil droplets whilst the hydrophilic head exists in the aqueous solution. When agitated, micelles then form around the oil droplets, with the non-polar nature of the micelle inside preventing its combination with water. The micelle heads are also negatively charged, causing any adjacent micelles to repel, breaking up grease/oil particles into water soluble micelles. These micelles are then washed away in the water.

116
Q

How can micelle formation be used for drug transport?

A

Polymers with a hydrophilic end and a hydrophobic end can be used to create micelles. Polymers micelles are excellent mediums to transport non-polar drugs around the body. Blood being an aqueous medium would not readily transport non-polar compounds around the body. Positioning a non-polar drug in the centre of a hydrophobic micelles leads to the negatively charged hydrophilic heads be able to interact with the aqueous blood. Consequently, allowing for the transport of non-polar drugs using micelle capsule within blood.

117
Q

What are amino acids?

A

Amino acids are the monomers of proteins and enzymes.

118
Q

What are the common characteristics of amino acids?

A

Each amino acid contains a central carbon atom with an amine functional group, carboxyl functional group, hydrogen atom, and an R group side chain.

119
Q

How do amino acids differ?

A

The only difference in all amino acids is the composition of the R group side chain.

120
Q

Why are amino acids simultaneously acidic and basic?

A

Amino acids have both an acidic functional group (-COOH) and a basic functional group (-NH2). The carboxylic acid can donate protons, and the amine can accept protons. This means that amino acids are in a constant flux between its ionic zwitterion form and its “neutral” form, depending on pH.

121
Q

What does zwitterion form mean? At what pH does this occur?

A

In zwitterion form, occurring at pH 7, the amino acid will a donate hydrogen (proton) atom from the hydroxyl group and attach it to the amine group. This creates a negative charge on the once hydroxyl group and a positive charge on the amine.

122
Q

What does an acidic versus basic environment do to the zwitterion?

A

In a low pH, hydrogen ions are present on the carboxylic acid as well as an additional one on the amine (causing a positive charge). In high pH, hydrogen ions are not present within the carboxylic acid and no additional protons are present on the amine either.

123
Q

What is the purpose of zwitterions?

A

Zwitterions maximise the number of protons that can be donated/received.

124
Q

How are peptide links formed?

A

Amino acid groups are linked by peptide bonds between carboxylic acids and amines, through a condensation reaction. The hydroxyl group from the carboxylic acid on one amino acid joins with a hydrogen from the amine on another amino acid, to form water and join the two peptides into a dipeptide.

125
Q

What are proteins?

A

Proteins are very large molecules containing different amino acids joined together by peptide bonds.

126
Q

How does the bonding within a protein determine its functionality?

A

The amide functional group and any said chains containing an amine, carbonyl group, carboxylic acid or hydroxyl group can undergo hydrogen bonding to other functional groups on the same protein, different proteins or water. This dictates how the peptide bends to form its protein structure.

127
Q

What are the four levels of protein structure and what are they dictated by?

A

Primary, secondary, tertiary and quaternary. The four levels of protein structure are dictated by the intermolecular interactions (hydrogen bonding) that can be formed between amino acid residues with a polypeptide chain.

128
Q

What is the composition of primary protein structure?

A

The linear sequence of amino acids linked together by a single polypeptide chain (no folds or intermolecular interactions).

129
Q

What is the composition of secondary protein structure?

A

The structure of localized regions of the polypeptide chain. The most common structures are α–helices and β–pleated sheets.
α-helix: a spiral shape held together by hydrogen bonding between the –NH group of a peptide bond and a –C=O group of a peptide bond four amino acids along in the chain.
β-pleated sheet: two adjacent regions of the polypeptide chain form a pleated structure held together by hydrogen-bonding between the –NH groups and –C=O groups in the peptide bonds.

130
Q

What is the composition of tertiary protein structure?

A

The 3D structure of a single polypeptide chain. This is determined by covalent bonds (disulfide bridges), ionic bonds, and secondary interactions (hydrogen bonding and dispersion forces) between the amino acid side chains within the same polypeptide chain.

131
Q

What is the composition of quaternary protein structure?

A

The three-dimensional structure of several polypeptide chains packed together.

132
Q

What is protein denaturation and how does it occur?

A

A protein’s structure ultimately determine its function as its 3D shape of a protein controls its ability to interacts with other molecules. As changes in temperature or pH can directly affect how a peptide chain may undergo secondary interactions (disrupting them), the structure is altered. This in turn affects the protein ability to function as the protein is denatured.

133
Q

How does pH change influence protein denaturation?

A

The environmental pH surrounding the protein will affect any of the -NH2 and -COOH functional groups and, consequently, the ionic bonds and hydrogen bonds in the protein.

134
Q

How does a decrease in pH affect the ionic bond controlled by the amine and carboxylic acids, within proteins?

A

A decrease in pH maximises the presence of protons meaning the amine gains a hydrogen atom and becomes positively charged, and the carboxylate ion gains a proton to become neutral. As there is now only a positive charge present, the ionic bond is broken.

135
Q

How does an increase in pH affect the ionic bond controlled by the amine and carboxylic acids, within proteins?

A

An increase in pH minimises the presence of protons meaning the initially positively charged amine loses a hydrogen atom and becomes neutral, and the carboxylic acid loses a proton to become negative. As there is now only a negative charge present, the ionic bond is broken.

136
Q

How does temperature change influence protein denaturation?

A

Increasing the temperature of the protein increases the kinetic energy of the atoms, destabilising the secondary interactions which disrupts the shape of the protein.

137
Q

What are polymers?

A

Polymers are large molecules made up of many monomers (repeating units) joined together.

138
Q

How are polymers named?

A

Polymers are names by adding the prefix “poly-“ to the name of the monomer.

139
Q

What are the two main reactions used to form polymers?

A

Addition reactions and condensation reactions.

140
Q

What are addition polymers and what are the conditions of addition reactions?

A

Addition polymers are formed through addition polymerisation (the linking of monomers together). Monomers containing carbon-carbon double bonds will be broken to form a single-bonded backbone. A catalyst, heat and pressure are required due to the energy required to remove double bonds.

141
Q

What are condensation polymers and what are the conditions of condensation reactions?

A

Condensation polymers are formed through condensation polymerisation (the linking of monomers together). The monomers combined in condensation polymerisation must contain two different functional groups that can undergo a condensation reaction (-OH and -COOH, or -NH2 and -COOH). Water is produced during this reaction, and the condensation polymer will contain esters or amides.

142
Q

How to tell the difference between addition and condensation polymers?

A

MONOMERS
Addition: -C=C-
Condensation: Two functional groups (-OH and -COOH, or -NH2 and -COOH)

POLYMER
Addition: -C-C-C-C-C-C- (backbone)
Condensation: Either ester of amide functional groups between repeating units

143
Q

What are polyesters and how are they produced?

A

Polyesters are products of condensation reactions with hydroxyl and carboxylic acids, and contain ester functional groups that link monomers together in a polymer.

144
Q

What are polyamides and how are they produced?

A

Polyamides are products of condensation reactions with amine and carboxylic acids, and contain amide functional groups that link monomers together in a polymer.

145
Q

What are the customisable features of a polymer?

A
  • chain length
  • branching side chains
  • cross-linking
  • polarity of side chains
  • additives such as dyes and UV adsorbers

These are all related to protein structure.

146
Q

What is the difference between natural and synthetic polymers?

A

Natural polymers are made by plants or animals (hair, silk DNA and starch). Synthetic polymers are manmade and have a wide variety of uses as they can be customised to have specific properties (plastics, fibres, paints, lubricants, adhesives and foams).

147
Q

What are the advantages and disadvantages of synthetic polymers?

A

ADVANTAGES
As synthetic polymer properties can be tailored, they have become used in the place of more traditional materials (i.e. metals and glass) and in place of natural polymers (i.e. cotton and wool). This allows them to be made cheaper, less dense, and more durable.

DISADVANTAGES
Synthetic polymers are susceptible to UV degradation, heat sensitive, and non-biodegradable.

148
Q

What is the bonding between polymer chains determined by?

A

Bonding between polymer chains is determined by the polarity of branching group (side chains) and the main chain links.

149
Q

Dispersion Forces within Polymers

A

Dispersion forces are present between polymer chains with non-polar side groups and non-polar main chain links (i.e. addition polymers). As the length of the polymer chain increases, the strength of dispersion forces also increases (larger MW = stronger dispersion forces). Polymers that only have dispersion forces between chains are soft, flexible and non-elastic (can be stretched out of shape) They also have low melting and softening points and can be reshaped with heat.

150
Q

What type of intermolecular force is present in all polymers?

A

Dispersion forces are present in all polymers but dispersion forces are weak and insignificant compared to hydrogen bonding and covalent bonding.

151
Q

Hydrogen Bonding within Polymers

A

Hydrogen bonding is present between polymer chains containing amines/amides, hydroxyl groups and carbonyl groups in the side or main chain links (i.e. condensation polymers). Hydrogen bonds are strong than dispersion forces meaning the resulting polymers are stronger, more rigid and more elastic than polymers with only dispersion forces between chains.

152
Q

Covalent Bonding (Cross-Links) within Polymers

A

Covalent bonds between polymer chains are called cross-links. As the number of cross-links increases, the rigidity, elasticity and hardness of the polymer increases. Cross links can be formed during polymerisation or after polymerisation with a cross linking agent.

153
Q

What are the characteristics of thermoplastics?

A
  • contain dispersion forces or hydrogen bonding between polymer chains
  • soften when heated, harden and become more rigid when cooled
  • can be recycled by heating and reshaping
154
Q

What are the characteristics of thermosets?

A
  • contain a high degree of cross-linking
  • will char or burin if heated sufficiently as covalent bonds break and the polymer decomposes
  • cannot be recycled
155
Q

What are the advantages and disadvantages of producing polymers?

A

Most synthetic polymers are produced from petrochemicals (chemicals produced using a petroleum feedstock).

ADVANTAGES
- fossil fuels are a relatively abundant feedstock
- petroleum is relatively easily extracted and processed
- there are existing industries, infrastructure and processing techniques for producing polymers from petroleum
- wide variety of polymers able to be produced from petroleum

DISADVANTAGES
- petroleum is a non-renewable resource/feedstock
- the reserves of petroleum are being used at a much faster rate than they are being naturally replenished

156
Q

What is a possible way of developing synthetic polymers from a renewable resource?

A

Since petrol is a fossil fuel (non-renewable source), research is being undertaken to develop synthetic biopolymers, which are derived from plants (biomass). Examples include starch and cellulose (polysaccharides), and proteins and oils (triglycerides).

157
Q

What are the advantages and disadvantages of biomass derived polymers?

A

ADVANTAGES
- plants/crops are a renewable feedstock
-plants/crops are a relatively abundant feedstock
-plants/crops are easily extracted and processed
- by-products or waste products from farming crops can be used as the source of biomass

DISADVANTAGES
- new area of research with limited number of synthetic biopolymers currently being produced
- production of synthetic biopolymers from plants/crops may compete directly with land for food production

158
Q

What are biodegradable polymers?

A

Biodegradable polymers can be broken down naturally in the environment. These include all natural polymers (cotton, cellulose, nucleic acids, proteins) and some synthetic polymers (mainly condensation polymers).

159
Q

What are the characteristics of biodegradable polymers that make them biodegradable?

A

Polymers containing ester (-COO-) or amide (-CONH-) functional groups can be hydrolysed causing the polymer to break down into smaller molecules. These smaller molecules are oligomers (multiple monomer units), dimers (two monomer units ) or monomers. Hydrolysis is catalysed by enzymes secreted from microorganisms such as bacteria and fungi.

160
Q

How can light sensitivity be used to create more biodegradable polymers?

A

Installing light sensitive molecules or carbonyl groups (C=O) into polymers make polymers photodegradable. A large number of carbonyl groups and light sensitive molecules will break down when exposed to UV light. This characteristic can be installed during synthesis process to ensure biodegradable properties.

161
Q

Explain how increasing temperature affects the biological function of an enzyme.

A

Increasing temperature increases the kinetic energy of atoms within the enzyme. This energy is sufficient enough to overcome the intermolecular bonds within the enzyme, distabilising and denaturing it. Therefore, the secondary, tertiary and quaternary structure of the enzyme is affected, disrupting the enzyme’s biological function.

Stage 2 Chemistry (4 decks)

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